Actually it's very likely they did meet... They were in the "Persephone Correctional Facility" at about the same time... In all likelihood though, she probably tried to convince Johnny to join her little cult and when he proved resistant to her methods, she threw him to Fontaine...

Stanley sold them both out in spite of the fact that he actually idolized Johnny... I think Sofia did Johnny a favor shooting him in the head... By doing that she allowed him to regain control of himself, he no longer slogged through what remained of his life a captive of his own mind... I think the whole reason she's so afraid of him is because she remembers throwing him to Fontaine and though she's remorseful about it, she doesn't know what he'll do if he can actually get to her without anyone or anything in his way...

LIKE LIKE LIKE JOHNNY I LOVE YOU THAT'S AMAZING. I could see that...Johnny Topside being like a huge flirt...DAMN THAT'S JUST CLASSIC. He has the looks! He can pull it offf. Maybe that's why he was in the jail LOL jk.